Gene glyphs are not rendering

[shashankbrgowda]

We are not rendering any glyph if the parent feature is 'gene' and its sub-feature is not equal to 'mRNA'

example gff

ctgA	example	gene	1050	9000	.	+	.	ID=EDEN;Name=EDEN;Note=protein kinase
ctgA	example	V_gene_segment	1050	9000	.	+	.	ID=EDEN.1;Parent=EDEN;Name=EDEN.1;Note=Eden splice form 1;Index=1
ctgA	example	five_prime_UTR	1050	1200	.	+	.	Parent=EDEN.1
ctgA	example	CDS	1201	1500	.	+	0	Parent=EDEN.1
ctgA	example	CDS	3000	3902	.	+	0	Parent=EDEN.1
ctgA	example	CDS	5000	5500	.	+	0	Parent=EDEN.1
ctgA	example	CDS	7000	7608	.	+	0	Parent=EDEN.1
ctgA	example	three_prime_UTR	7609	9000	.	+	.	Parent=EDEN.1

[shashankbrgowda]

[garrettjstevens]

Just to clarify the expected behavior here, since "V_gene_segment" is not a valid child in the ontology of "gene", this should use the fallback glyph and not a gene glyph.

[dariober]

Also the GFF below doesn't show any glyph even if it has gene -> mRNA -> exon

##gff-version 3
ctgA	example	gene	1	100	.	+	.	ID=gx1
ctgA	example	mRNA	1	100	.	+	.	ID=tx1;Parent=gx1
ctgA	example	exon	1	100	.	+	.	ID=exon1;Parent=tx1
ctgA	example	gene	100	200	.	+	.	ID=gx2
ctgA	example	mRNA	100	200	.	+	.	ID=tx2;Parent=gx2
ctgA	example	exon	100	200	.	+	.	ID=exon2;Parent=tx2
##FASTA
>ctgA
cattgttgcggagttgaacaACGGCATTAGGAACACTTCCGTCTCtcacttttatacgat
tatgattggttctttagccttggtttagattggtagtagtagcggcgctaatgctacctg
aattgagaactcgagcgggggctaggcaaattctgattcagcctgacttctcttggaacc
ctgcccataaatcaaagggttagtgcggccaaaacgttggacaacggtattagaagacca
acctgaccaccaaaccgtcaattaaccggtatcttctcggaaacggcggttctctcctag
atagcgatctgtggtctcaccatgcaatttaaacaggtgagtaaagattgctacaaatac
gagactagctgtcaccagatgctgttcatctgttggctccttggtcgctccgttgtaccc
aggctactttgaaagagcgcagaatacttagacggtatcgatcatggtagcatagcattc
tgataacatgtatggagttcgaacatccgtctggggccggacggtccgtttgaggttggt
tgatctgggtgatagtcagcaagatagacgttagataacaaattaaaggattttacctta
gattgcgactagtacaacggtacatcggtgattcgcgctctactagatcacgctatgggt
accataaacaaacggtggaccttctcaagctggttgacgcctcagcaacataggcttcct
cctccacgcatctcagcataaaaggcttataaactgcttctttgtgccagagcaactcaa
ttaagcccttggtaccgtgggcacgcattctgtcacggtgaccaactgttcatcctgaat
cgccgaatgggactatttggtacaggaatcaagcggatggcactactgcagcttatttac
gacggtattcttaaagtttttaagacaatgtatttcatgggtagttcggtttgttttatt
gctacacaggctcttgtagacgacctacttagcactacggccgagcgcaataacccccgg
aaagcacttgctactgggaggcgggtttatccatcggcaataggggttatcagtactacc
aagaagattgtgaagatattaacagcattgaaaaaagttcggactgggcatgaaacgtgt

[shashankbrgowda]

CDS is not rendered when mRNA has exons and CDS doesn't contain discontinuous location.

When a feature contain exon, glyph is rendered using CanonicalGeneGlyph. CanonicalGeneGlyph doesn't render CDS if it doesn't contain discontinuous locations.

[shashankbrgowda]

User request: Ability to render operon - union of genes. It seems like operon is not rendered in jbrowse at all and apollo track renders it as GenericChildGlyph.

Apollo track:

Jbrowse lgv track:

GFF:

contig_2	Prodigal:002006	operon	664	1426	.	-	0	ID=operon1;name=test_operon
contig_2	Prodigal:002006	gene	664	855	.	-	0	ID=BU_ATCC8492_00002;inference=ab initio prediction:Prodigal:002006;locus_tag=BU_ATCC8492_00002;product=hypothetical protein;eggNOG=411479.BACUNI_00026;COG=-;KEGG=-;Parent=operon1
contig_2	Prodigal:002006	gene	842	1426	.	-	0	ID=BU_ATCC8492_00003;inference=ab initio prediction:Prodigal:002006;locus_tag=BU_ATCC8492_00003;product=hypothetical protein;eggNOG=411479.BACUNI_00025;COG=S;KEGG=-;Pfam=PF06414;InterPro=IPR010488,IPR027417,-;Parent=operon1
contig_2	Prodigal:002006	mRNA	664	1426	.	-	0	ID=transcript:BU_ATCC8492_00003;inference=ab initio prediction:Prodigal:002006;locus_tag=BU_ATCC8492_00003;product=hypothetical protein;eggNOG=411479.BACUNI_00025;COG=S;KEGG=-;Pfam=PF06414;InterPro=IPR010488,IPR027417,-;Parent=BU_ATCC8492_00002,BU_ATCC8492_00003
contig_2	Prodigal:002006	exon	664	1426	.	-	0	ID=exon:BU_ATCC8492_00003;inference=ab initio prediction:Prodigal:002006;locus_tag=BU_ATCC8492_00003;product=hypothetical protein;eggNOG=411479.BACUNI_00025;COG=S;KEGG=-;Pfam=PF06414;InterPro=IPR010488,IPR027417,-;Parent=transcript:BU_ATCC8492_00003
contig_2	Prodigal:002006	CDS	664	855	.	-	0	ID=CDS:BU_ATCC8492_00002;inference=ab initio prediction:Prodigal:002006;locus_tag=BU_ATCC8492_00002;product=hypothetical protein;eggNOG=411479.BACUNI_00026;COG=-;KEGG=-;Parent=transcript:BU_ATCC8492_00003;Derives_from=BU_ATCC8492_00002
contig_2	Prodigal:002006	CDS	842	1426	.	-	0	ID=CDS:BU_ATCC8492_00003;inference=ab initio prediction:Prodigal:002006;locus_tag=BU_ATCC8492_00003;product=hypothetical protein;eggNOG=411479.BACUNI_00025;COG=S;KEGG=-;Pfam=PF06414;InterPro=IPR010488,IPR027417,-;Parent=transcript:BU_ATCC8492_00003;Derives_from=BU_ATCC8492_00003

[garrettjstevens]

Gene glyph rendering fixed in #412, and operon rendering now tracked in #440